There's more to a "best movie" then just the integration of action and story. Acting performance, cinematography and direction are just three of the many factors that come in to play for making a great movie. Episode II didn't score well in any of these catagories and the Academy of Motion Picture, Science and Arts didn't think that well of them either.
As far as I know, the version released on DVD next september will be the '97 Special Edition with some additions and alterations.
According to The Digital Bits the shot with the Emperor in TESB will be altered and finally match the Emperor in ROTJ (why didn't Lucas do this for the Special Edition in the first place?). The Jabba creature in the Mos Eisley hangar scene was never up to standards and I've always wondered how this scene made it into the Special Edition, considering Lucas being such a perfectionist and 'quality freak'. He'd better left it out again (it doens't add much to the story anyway), but instead he'll 'improve' the scene using a better CGI model (and off course 6-7 years worth of software improvements). If these were all the changes he's making to the Special Edition, I could live with that (except for the Greedo shoots first thing). But I'm afraid he won't leave it with that...
While work on the '79 Special Editions progressed, the official Star Wars website was very informative on the changes and 'improvements' made to the original version. For the DVD release there has been NO official word (yet) on the changes that no doubt will b made to the movies. We'll just have to wait and see...